Contacts of the helix formed by residues 62 - 73 (chain F) in PDB entry 5ANC
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 62 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1F MET* 5.2 0.4 - - - -
29F ALA* 3.7 3.1 - - - +
30F LYS* 3.0 34.5 + - - +
31F ILE* 3.3 13.2 + - - +
60F LEU 4.0 0.6 + - - -
61F SER* 1.3 70.5 - - - +
63F GLU* 1.3 61.2 - - - +
65F ILE* 3.2 6.3 + - - +
66F GLU* 2.9 27.9 + - - +
93F PRO* 3.3 29.8 - - - +
125F THR* 3.2 23.7 + - - -
126F VAL* 4.4 0.6 - - - +
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Residues in contact with GLU 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1F MET* 2.6 56.0 + - - +
2F GLY 4.3 0.7 + - - -
30F LYS* 3.7 30.5 - - + +
61F SER* 3.8 13.2 - - - -
62F SER* 1.3 78.7 - - - +
64F ALA* 1.3 64.5 + - - +
66F GLU* 3.2 6.9 + - - +
67F ALA* 2.9 29.5 + - - +
3185N C 4.8 0.7 + - - -
3186N G 3.0 37.7 + - - +
3187N C 2.9 17.8 + - - -
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Residues in contact with ALA 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60F LEU* 4.9 1.6 - - + -
61F SER* 3.3 24.0 + - - +
62F SER 3.2 0.2 - - - -
63F GLU* 1.3 81.3 - - - +
65F ILE* 1.3 58.1 + - - +
67F ALA* 3.2 4.3 + - - +
68F GLY 2.9 24.6 + - - -
158F LYS 4.1 9.2 - - - +
159F PHE* 3.4 16.4 - - + -
160F PRO* 5.2 2.5 - - + -
3186N G 3.8 30.1 - - - +
3187N C 4.2 7.4 - - - +
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Residues in contact with ILE 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31F ILE* 3.5 24.5 - - + -
60F LEU* 4.3 9.6 - - + +
61F SER 3.0 22.2 + - - +
62F SER* 3.2 8.0 + - - +
64F ALA* 1.3 76.5 - - - +
66F GLU* 1.3 55.4 + - - +
68F GLY* 3.2 2.8 + - - -
69F ARG* 2.9 25.9 + - + +
89F VAL* 3.8 24.2 - - + -
91F VAL* 3.7 32.8 - - + +
93F PRO* 4.3 10.1 - - + -
127F ALA* 4.2 15.9 - - + -
136F PHE* 3.6 6.5 - - + -
159F PHE* 3.7 18.2 - - + -
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Residues in contact with GLU 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F LYS* 4.0 10.5 - - + +
31F ILE* 3.1 31.5 - - + +
33F ILE* 5.6 0.2 - - - +
62F SER 2.9 11.2 + - - +
63F GLU* 3.3 13.7 - - - +
65F ILE* 1.3 76.6 - - - +
67F ALA* 1.3 64.5 + - - +
69F ARG* 3.0 34.4 + - - +
70F ILE* 3.0 36.3 + - + +
3185N C 5.0 5.8 - - - +
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Residues in contact with ALA 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63F GLU 2.9 11.2 + - - +
64F ALA* 3.2 9.6 + - - +
66F GLU* 1.3 78.3 - - - +
68F GLY* 1.3 62.4 + - - +
70F ILE* 3.2 22.6 + - - +
71F SER 3.2 9.5 + - - -
158F LYS* 3.6 19.4 - - + +
3185N C 3.8 19.1 - - - +
3186N G 3.5 28.9 - - - +
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Residues in contact with GLY 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64F ALA 2.9 13.7 + - - -
65F ILE 3.2 4.0 + - - -
67F ALA* 1.3 74.8 - - - +
69F ARG* 1.3 62.8 + - - +
71F SER* 3.1 19.2 + - - -
72F CYS* 3.5 5.2 + - - -
136F PHE* 3.6 15.5 - - - -
155F SER* 3.7 11.3 + - - -
158F LYS* 4.3 15.2 - - - +
159F PHE* 4.2 7.9 - - - -
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Residues in contact with ARG 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31F ILE* 4.4 9.0 - - + -
33F ILE* 3.6 54.7 + - - +
34F PHE* 5.3 3.5 - - - +
35F ASP 4.5 1.2 + - - -
36F LEU* 3.4 48.9 - - + +
65F ILE 2.9 9.9 + - - +
66F GLU* 3.0 41.6 + - - +
68F GLY* 1.3 76.3 - - - +
70F ILE* 1.3 67.9 + - + +
71F SER 3.2 0.2 - - - -
72F CYS* 3.2 5.0 + - - +
73F ASN* 2.8 24.9 + - - -
87F MET* 4.8 0.9 - - - -
89F VAL* 5.2 3.8 - - + -
136F PHE* 3.2 25.7 - - + -
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Residues in contact with ILE 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66F GLU* 3.0 37.3 + - + +
67F ALA* 3.2 19.0 + - - +
69F ARG* 1.3 89.0 - - + +
71F SER* 1.3 57.8 + - - +
73F ASN* 3.7 21.1 - - + +
74F LYS* 3.5 27.4 - - - +
154F ARG* 4.5 2.4 + - - -
3171N A 5.4 1.0 - - - +
3184N A 5.2 14.2 - - + +
3185N C 4.6 20.2 - - - +
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Residues in contact with SER 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67F ALA 3.2 2.0 + - - -
68F GLY 3.1 12.4 + - - -
70F ILE* 1.3 72.4 - - - +
72F CYS* 1.3 54.7 + - - +
73F ASN 3.1 1.3 - - - -
74F LYS* 2.8 25.1 + - - +
75F TYR* 2.8 18.5 + - - +
151F ALA* 4.2 1.1 - - - -
154F ARG* 3.5 50.6 + - - +
155F SER* 4.2 7.0 - - - -
158F LYS* 3.4 24.5 - - - +
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Residues in contact with CYS 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36F LEU* 5.0 0.9 - - - -
68F GLY 3.8 6.1 - - - -
69F ARG 3.2 7.7 + - - +
71F SER* 1.3 79.5 - - - +
73F ASN* 1.3 58.7 + - - +
75F TYR 3.0 20.4 - - - +
76F ILE* 4.2 0.9 - - - +
85F PHE* 3.3 20.1 - - + -
87F MET* 3.4 37.5 - - + -
136F PHE* 5.2 1.3 - - - -
138F ILE* 4.9 2.2 - - - -
151F ALA* 3.8 28.9 - - + -
152F LEU* 4.4 3.6 - - - -
155F SER* 3.1 27.4 - - - -
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Residues in contact with ASN 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36F LEU* 3.9 30.8 - - + +
69F ARG* 2.8 16.6 + - - +
70F ILE* 3.7 19.4 - - + +
72F CYS* 1.3 77.6 - - - +
74F LYS* 1.3 78.0 + - + +
76F ILE* 3.0 38.6 - - - +
85F PHE* 5.8 0.2 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il